Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007840.1 Hibiscus syriacus cultivar Beakdansim tig00110194_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1104544
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:830451 original size:23 final size:24
Alignment explanation
Indices: 830408--830454 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
830398 ATATGGCATG
*
830408 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
830432 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
830455 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:830706 original size:31 final size:31
Alignment explanation
Indices: 830668--830852 Score: 295
Period size: 31 Copynumber: 6.0 Consensus size: 31
830658 AGGGTCGAGG
830668 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
830699 GTTTACCTATGTTCTTCGGG--ATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
830728 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
830759 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
830790 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
830821 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
830852 G
1 G
830853 GTCCTTCGGG
Statistics
Matches: 144, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
29 29 0.20
31 114 0.79
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:833979 original size:21 final size:21
Alignment explanation
Indices: 833953--833998 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
833943 GAGTTCTGGG
* *
833953 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
833974 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
833995 CAAG
1 CAAG
833999 CGACAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:834672 original size:23 final size:24
Alignment explanation
Indices: 834629--834675 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
834619 ATATGGCATG
*
834629 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
834653 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
834676 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:834929 original size:31 final size:31
Alignment explanation
Indices: 834891--835077 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
834881 AGGGTCGAGG
834891 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
834922 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
834953 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
834984 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
835015 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
835046 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
835077 G
1 G
835078 GTCCTTCGGG
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:841423 original size:21 final size:21
Alignment explanation
Indices: 841397--841450 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
841387 TTCCTTTCAC
841397 AGAGGATGAAGACAAACAAGG
1 AGAGGATGAAGACAAACAAGG
841418 AGAGGATGAAGACAAACAAGG
1 AGAGGATGAAGACAAACAAGG
* *
841439 AGTGGTTGAAGA
1 AGAGGATGAAGA
841451 AATAGCAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.48, C:0.07, G:0.35, T:0.09
Consensus pattern (21 bp):
AGAGGATGAAGACAAACAAGG
Found at i:843060 original size:67 final size:68
Alignment explanation
Indices: 842943--843100 Score: 250
Period size: 67 Copynumber: 2.4 Consensus size: 68
842933 GACATGGAAT
*
842943 GAAC-AGGAGGCTTCATTATGTACCATGTAATGCATTATCCACATCATCAATATAAGTTAACAAA
1 GAACGAGGA-GCTTCATCATGTACCATGTAATGCATTATCCACATCATCAATATAAGTTAACAAA
*
843007 TGAA
65 CGAA
* *
843011 GAA-GAGGAGCTTCATCATGTATCATGTAATGCATTATCCACATCATCAATATACGTTAACAAAC
1 GAACGAGGAGCTTCATCATGTACCATGTAATGCATTATCCACATCATCAATATAAGTTAACAAAC
843075 GAA
66 GAA
843078 GAACG-GGAGCTTCATCATGTACC
1 GAACGAGGAGCTTCATCATGTACC
843101 CTTTTAACAC
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
67 75 0.90
68 8 0.10
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (68 bp):
GAACGAGGAGCTTCATCATGTACCATGTAATGCATTATCCACATCATCAATATAAGTTAACAAAC
GAA
Found at i:855585 original size:28 final size:28
Alignment explanation
Indices: 855553--855607 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
855543 TTTGGTATAA
* * *
855553 CTAATGCTTCCTTGAGCAACTCTGTAAT
1 CTAATGCCTCCTTGAGAAACTCAGTAAT
855581 CTAATGCCTCCTTGAGAAACTCAGTAA
1 CTAATGCCTCCTTGAGAAACTCAGTAA
855608 CCTTAGTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (28 bp):
CTAATGCCTCCTTGAGAAACTCAGTAAT
Found at i:859152 original size:2 final size:2
Alignment explanation
Indices: 859147--859176 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
859137 TGTGTATCTT
859147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
859177 AAGATTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:866952 original size:28 final size:28
Alignment explanation
Indices: 866912--866969 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
866902 TCACAGAACA
866912 CCGTCCTTGCCCCCATTCTCCCAAGCAT
1 CCGTCCTTGCCCCCATTCTCCCAAGCAT
866940 CCGTCCTTGCCCCCATTCTCCCAAGCAT
1 CCGTCCTTGCCCCCATTCTCCCAAGCAT
866968 CC
1 CC
866970 ATGGGTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.52, G:0.10, T:0.24
Consensus pattern (28 bp):
CCGTCCTTGCCCCCATTCTCCCAAGCAT
Found at i:874413 original size:18 final size:17
Alignment explanation
Indices: 874382--874415 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
874372 CAAATTTTCA
*
874382 AAAATTAAATTTTAATT
1 AAAATTAAAATTTAATT
874399 AAAATTAAGAATTTAAT
1 AAAATTAA-AATTTAAT
874416 ATTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAAATTAAAATTTAATT
Found at i:883369 original size:2 final size:2
Alignment explanation
Indices: 883362--883386 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
883352 ACATGAGGGG
883362 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
883387 ACCAAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:888879 original size:90 final size:90
Alignment explanation
Indices: 888726--888908 Score: 366
Period size: 90 Copynumber: 2.0 Consensus size: 90
888716 GAGGAGAACG
888726 AGAGCAAATTATAAAAGTCAAGTGGCCTATTATGATATTGTCAAAAATATTTAAAGCAACAAGAG
1 AGAGCAAATTATAAAAGTCAAGTGGCCTATTATGATATTGTCAAAAATATTTAAAGCAACAAGAG
888791 AAACAACCAGTCCAATTCAGATAAA
66 AAACAACCAGTCCAATTCAGATAAA
888816 AGAGCAAATTATAAAAGTCAAGTGGCCTATTATGATATTGTCAAAAATATTTAAAGCAACAAGAG
1 AGAGCAAATTATAAAAGTCAAGTGGCCTATTATGATATTGTCAAAAATATTTAAAGCAACAAGAG
888881 AAACAACCAGTCCAATTCAGATAAA
66 AAACAACCAGTCCAATTCAGATAAA
888906 AGA
1 AGA
888909 TGTTATTCAG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (90 bp):
AGAGCAAATTATAAAAGTCAAGTGGCCTATTATGATATTGTCAAAAATATTTAAAGCAACAAGAG
AAACAACCAGTCCAATTCAGATAAA
Found at i:892595 original size:161 final size:162
Alignment explanation
Indices: 892408--892732 Score: 634
Period size: 161 Copynumber: 2.0 Consensus size: 162
892398 CAAGACCGGA
892408 TTATGATATGAAATTGATTTTGGTAAAAGGCATTGTGAAATCCTAGGAAAGCTGTTCAAAAATCT
1 TTATGATATGAAATTGATTTTGGTAAAAGGCATTGTGAAATCCTAGGAAAGCTGTTCAAAAATCT
892473 GCCACAAATTAGAAATCGATCTAGTCTAACCCATGTTGACAACTCTCTATTACTGCACCAGGTGA
66 GCCACAAATTAGAAATCGATCTAGTCTAACCCATGTTGACAACTCTCTATTACTGCACCAGGTGA
892538 AAATTCCTCCTG-ATAGGCAGATCCATAAGGT
131 AAATTCCTCCTGAATAGGCAGATCCATAAGGT
892569 TTATGATATGAAATTGATTTTGGTAAAAGGCATTGTGAAATCCTAGGAAAGCTGTTCAAAAATCT
1 TTATGATATGAAATTGATTTTGGTAAAAGGCATTGTGAAATCCTAGGAAAGCTGTTCAAAAATCT
892634 GCCACAAATTAGAAATCGATCTAGTCTAACCCATGTTGACAACTCTCTATTACTGCACCAGGTGA
66 GCCACAAATTAGAAATCGATCTAGTCTAACCCATGTTGACAACTCTCTATTACTGCACCAGGTGA
892699 AAATTCCTCCTGACATAGGCAGATCCATAAGGT
131 AAATTCCTCCTGA-ATAGGCAGATCCATAAGGT
892732 T
1 T
892733 AGCTTGTATA
Statistics
Matches: 162, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
161 142 0.88
163 20 0.12
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (162 bp):
TTATGATATGAAATTGATTTTGGTAAAAGGCATTGTGAAATCCTAGGAAAGCTGTTCAAAAATCT
GCCACAAATTAGAAATCGATCTAGTCTAACCCATGTTGACAACTCTCTATTACTGCACCAGGTGA
AAATTCCTCCTGAATAGGCAGATCCATAAGGT
Found at i:895179 original size:411 final size:410
Alignment explanation
Indices: 894417--895235 Score: 1586
Period size: 411 Copynumber: 2.0 Consensus size: 410
894407 AGGACTTGCT
894417 ACCCTTAACAGTAATCTCGCTGATGAAAGATCATCTCTATTCTATGTCTCCTCCATGATACTCAC
1 ACCCTTAACAGTAATCTCGCTGATGAAAGATCATCTCTATTCTATGTCTCCTCCATGATACTCAC
*
894482 AAGCTCTCCCCACATTCCTGCAAGTTTCTATATAAAAGGTGCAGACCAACTAAGAAATGGTAGCC
66 AAGCTCTCCCCACATTCCTGCAAGTTTCTACATAAAAGGTGCAGACCAACTAAGAAATGGTAGCC
894547 CCACCAACTCTACCAAGCAGTACGCCAATGAAACTCCTTCGTTTAACAATGGAGATAACCACTTA
131 CCACCAACTCTACCAAGCAGTACGCCAATGAAACTCCTTCGTTTAACAATGGAGATAACCACTTA
894612 AACCAGAGGAACAACTTCTCTCTAATGTTCGACCAAGCCTTTAAGAAATCTTCATTAGAACTGAA
196 AACCAGAGGAACAACTTCTCTCTAATGTTCGACCAAGCCTTTAAGAAATCTTCATTAGAACTGAA
894677 TATAACGATACAAGCATTCTTAACATAACCACAGCTTACTATTCTGACCTCCTAACCCTCCTTCG
261 TATAACGATACAAGCATTCTTAACATAACCACAGCTTACTATTCTGACCTCCTAACCCTCCTTCG
894742 CCATGGCCTTTTTCACCATATCAGACTGAAGGGGATATTTCAAAACCCCTGTTAAAGAATTCTTC
326 CCATGGCCTTTTTCACCATATCAGACTGAAGGGGATATTTCAAAACCCCTGTTAAAGAATTCTTC
894807 ACCCAGCTTGAATTCTTCAAA
391 ACCCAGCTTGAA-TCTTCAAA
*
894828 ACCCTTAACAGTAATCTCGCTGATGAAAGATCATCTCTATTCTTTGTCTCCTCCATGATACTCAC
1 ACCCTTAACAGTAATCTCGCTGATGAAAGATCATCTCTATTCTATGTCTCCTCCATGATACTCAC
894893 AAGCTCTCCCCACATTCCTGCAAGTTTCTACATAAAAGGTGCAGACCAACTAAGAAATGGTAGCC
66 AAGCTCTCCCCACATTCCTGCAAGTTTCTACATAAAAGGTGCAGACCAACTAAGAAATGGTAGCC
894958 CCACCAACTCTACCAAGCAGTACGCCAAT-AGAACTCCTTCGTTTAACAATGGAGATAACCACTT
131 CCACCAACTCTACCAAGCAGTACGCCAATGA-AACTCCTTCGTTTAACAATGGAGATAACCACTT
*
895022 AAACCAGAGGAACAACTTCTCTCTAATGTTTGACCAAGCCTTTAAGAAATCTTCATTAGAACTGA
195 AAACCAGAGGAACAACTTCTCTCTAATGTTCGACCAAGCCTTTAAGAAATCTTCATTAGAACTGA
895087 ATATAACGATACAAGCATTCTTAACATAACCACAGCTTACTATTCTGACCTCCTAACCCTCCTTC
260 ATATAACGATACAAGCATTCTTAACATAACCACAGCTTACTATTCTGACCTCCTAACCCTCCTTC
895152 GCCATGGCCTTTTTCACCATATCAGACTGAAGGGGATATTTCAAAACCCCTGTTAAAGAATTCTT
325 GCCATGGCCTTTTTCACCATATCAGACTGAAGGGGATATTTCAAAACCCCTGTTAAAGAATTCTT
895217 CACCCAGCTTGAATCTTCA
390 CACCCAGCTTGAATCTTCA
895236 GAAGGAATGT
Statistics
Matches: 404, Mismatches: 3, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
410 7 0.02
411 397 0.98
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (410 bp):
ACCCTTAACAGTAATCTCGCTGATGAAAGATCATCTCTATTCTATGTCTCCTCCATGATACTCAC
AAGCTCTCCCCACATTCCTGCAAGTTTCTACATAAAAGGTGCAGACCAACTAAGAAATGGTAGCC
CCACCAACTCTACCAAGCAGTACGCCAATGAAACTCCTTCGTTTAACAATGGAGATAACCACTTA
AACCAGAGGAACAACTTCTCTCTAATGTTCGACCAAGCCTTTAAGAAATCTTCATTAGAACTGAA
TATAACGATACAAGCATTCTTAACATAACCACAGCTTACTATTCTGACCTCCTAACCCTCCTTCG
CCATGGCCTTTTTCACCATATCAGACTGAAGGGGATATTTCAAAACCCCTGTTAAAGAATTCTTC
ACCCAGCTTGAATCTTCAAA
Found at i:898739 original size:61 final size:61
Alignment explanation
Indices: 898614--898772 Score: 146
Period size: 61 Copynumber: 2.6 Consensus size: 61
898604 ATTATTATCT
* * * * * * ** * *
898614 TCATTTTGAATTAATATTTAAA-TATTTAAATATTTTAGTTTCATCCTTAAATTATGACTA
1 TCATTTTGAATTGATCTCTAAACTTTTTGAATATTTCAGTTTCATCCCCAAACTATAACTA
* *
898674 TCATTTT-ATATTTATCT-TCAAATTTTTTGAATATTTCAGTTTCATCCCCAAACTATAATCT-
1 TCATTTTGA-ATTGATCTCT-AAACTTTTTGAATATTTCAGTTTCATCCCCAAACTATAA-CTA
*
898735 TCATTTTGAATTGATCTCTAAACTTTTTGAACATTTCA
1 TCATTTTGAATTGATCTCTAAACTTTTTGAATATTTCA
898773 AATCATCTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
59 2 0.02
60 16 0.20
61 59 0.73
62 4 0.05
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (61 bp):
TCATTTTGAATTGATCTCTAAACTTTTTGAATATTTCAGTTTCATCCCCAAACTATAACTA
Found at i:903547 original size:23 final size:23
Alignment explanation
Indices: 903521--903672 Score: 112
Period size: 23 Copynumber: 6.7 Consensus size: 23
903511 TTATATTCAA
* *
903521 GAACGCTAAATGAATATGTTCGC
1 GAACGCTAAACGAACATGTTCGC
** *
903544 GAACATTAAACGAACATGTTCAC
1 GAACGCTAAACGAACATGTTCGC
* *
903567 AAACGTTAAACGAACATGTTCGC
1 GAACGCTAAACGAACATGTTCGC
* **
903590 GAACGCTAAATG-A-ATGGGCGC
1 GAACGCTAAACGAACATGTTCGC
* * *
903611 GAACGTTAAGC-AAGCATGTTCAC
1 GAACGCTAAACGAA-CATGTTCGC
* * * **
903634 AAACGTTAAACGAACACGTTCAT
1 GAACGCTAAACGAACATGTTCGC
903657 GAACGCTAAACGAACA
1 GAACGCTAAACGAACA
903673 AACACGAACA
Statistics
Matches: 100, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
21 15 0.15
22 1 0.01
23 82 0.82
24 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (23 bp):
GAACGCTAAACGAACATGTTCGC
Found at i:903632 original size:67 final size:69
Alignment explanation
Indices: 903516--903666 Score: 200
Period size: 67 Copynumber: 2.2 Consensus size: 69
903506 TTCGTTTATA
* **
903516 TTCAAGAACGCTAAATGAATATGTTCGCGAACATTAAACGAACATGTTCACAAACGTTAAACGAA
1 TTCACGAACGCTAAATGAATATGGGCGCGAACATTAAACGAACATGTTCACAAACGTTAAACGAA
*
903581 CATG
66 CACG
* * *
903585 TTCGCGAACGCTAAATG-A-ATGGGCGCGAACGTTAAGC-AAGCATGTTCACAAACGTTAAACGA
1 TTCACGAACGCTAAATGAATATGGGCGCGAACATTAAACGAA-CATGTTCACAAACGTTAAACGA
903647 ACACG
65 ACACG
*
903652 TTCATGAACGCTAAA
1 TTCACGAACGCTAAA
903667 CGAACAAACA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
66 2 0.03
67 54 0.75
68 1 0.01
69 15 0.21
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (69 bp):
TTCACGAACGCTAAATGAATATGGGCGCGAACATTAAACGAACATGTTCACAAACGTTAAACGAA
CACG
Found at i:912406 original size:43 final size:44
Alignment explanation
Indices: 912345--912427 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 44
912335 GGAGAAAGGG
* * * *
912345 CTCAATTATATAGATAAAATGTAGGATT-ACAAAAATTAGAGGC
1 CTCAATTATAAAGATAAAAAGTAGAATTGAAAAAAATTAGAGGC
912388 CTCAATTATAAA-AGTAAAAAGTAGAATTGAAAAAAATTAG
1 CTCAATTATAAAGA-TAAAAAGTAGAATTGAAAAAAATTAG
912428 GGCTCTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.03
43 23 0.68
44 10 0.29
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (44 bp):
CTCAATTATAAAGATAAAAAGTAGAATTGAAAAAAATTAGAGGC
Found at i:927818 original size:16 final size:18
Alignment explanation
Indices: 927782--927819 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
927772 GATAACATTT
*
927782 TTTTGTGTCACATATATA
1 TTTTGTGTCACATACATA
927800 TTTTGTG-CA-ATACATA
1 TTTTGTGTCACATACATA
927816 TTTT
1 TTTT
927820 ATAAAACGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 2 0.11
18 7 0.37
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTTGTGTCACATACATA
Found at i:930311 original size:21 final size:21
Alignment explanation
Indices: 930285--930327 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
930275 AAAGTTCATC
930285 CATCATTGACAATTTGTGTTG
1 CATCATTGACAATTTGTGTTG
930306 CATCATTGACAATTTGTGTTG
1 CATCATTGACAATTTGTGTTG
930327 C
1 C
930328 TAATATAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (21 bp):
CATCATTGACAATTTGTGTTG
Found at i:934772 original size:19 final size:18
Alignment explanation
Indices: 934734--934772 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
934724 GATATACATG
* *
934734 AAGTTATTTTCATTTTAA
1 AAGTTATTTTCACTTCAA
934752 AAGTTATTTTTCACTTCAA
1 AAGTTA-TTTTCACTTCAA
934771 AA
1 AA
934773 ATGAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (18 bp):
AAGTTATTTTCACTTCAA
Found at i:942595 original size:2 final size:2
Alignment explanation
Indices: 942588--942634 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
942578 ACAACAAAAT
942588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
942630 TA TA T
1 TA TA T
942635 CCAGCCAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:944246 original size:33 final size:33
Alignment explanation
Indices: 944199--944311 Score: 111
Period size: 33 Copynumber: 3.4 Consensus size: 33
944189 CGAAGCCGAA
** *
944199 GCAAAGCCTGCAGAAGCTCAAGCTGAAGGAGAG
1 GCAAAGCCCACAGAAGCTCAAGCAGAAGGAGAG
* * * * *
944232 GCAAAGCCTACAGAAACTCCAGCAG-AGGCCGAA
1 GCAAAGCCCACAGAAGCTCAAGCAGAAGG-AGAG
* *
944265 GCAAAGCCCACGGAAGCTGAAGCAGAAGGAGAG
1 GCAAAGCCCACAGAAGCTCAAGCAGAAGGAGAG
*
944298 ACAAAGCCCACAGA
1 GCAAAGCCCACAGA
944312 GGCTGTTGCC
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 3 0.05
33 57 0.90
34 3 0.05
ACGTcount: A:0.40, C:0.26, G:0.29, T:0.05
Consensus pattern (33 bp):
GCAAAGCCCACAGAAGCTCAAGCAGAAGGAGAG
Found at i:947772 original size:13 final size:13
Alignment explanation
Indices: 947754--947778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
947744 GAACACATTT
947754 AAATTAATTATAC
1 AAATTAATTATAC
947767 AAATTAATTATA
1 AAATTAATTATA
947779 TAAAATATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAATTATAC
Found at i:959654 original size:54 final size:54
Alignment explanation
Indices: 959595--959702 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
959585 CGTTCACCCA
*
959595 CTAATCGATTATTACATTTTCTATTATCCCAAATACCTAAATACATAAATCCCT
1 CTAATCGATTATTACATTTTCTATCATCCCAAATACCTAAATACATAAATCCCT
* *
959649 CTAATCGATTATTACATTTTCTATCATCCCAAATTCCTAAATTCATAAATCCCT
1 CTAATCGATTATTACATTTTCTATCATCCCAAATACCTAAATACATAAATCCCT
959703 TCTCTTAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (54 bp):
CTAATCGATTATTACATTTTCTATCATCCCAAATACCTAAATACATAAATCCCT
Found at i:965831 original size:17 final size:18
Alignment explanation
Indices: 965811--965847 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
965801 TTAGATATTG
965811 TTTTA-AATAA-ATACATT
1 TTTTACAATAATA-ACATT
965828 TTTTACAATAATAACATT
1 TTTTACAATAATAACATT
965846 TT
1 TT
965848 CACCTCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 12 0.67
19 1 0.06
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTACAATAATAACATT
Found at i:968059 original size:13 final size:13
Alignment explanation
Indices: 968041--968065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
968031 AATATTTTAA
968041 TAATTATAAGATT
1 TAATTATAAGATT
968054 TAATTATAAGAT
1 TAATTATAAGAT
968066 AAAATGACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TAATTATAAGATT
Found at i:968319 original size:16 final size:17
Alignment explanation
Indices: 968298--968338 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
968288 GTAACCGGTT
968298 TCGG-TTTGAAAAAAAA
1 TCGGTTTTGAAAAAAAA
*
968314 TCGGTTTTTAAAAAAAA
1 TCGGTTTTGAAAAAAAA
*
968331 TCGATTTT
1 TCGGTTTT
968339 TAATCCGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (17 bp):
TCGGTTTTGAAAAAAAA
Found at i:968328 original size:17 final size:17
Alignment explanation
Indices: 968306--968341 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
968296 TTTCGGTTTG
*
968306 AAAAAAAATCGGTTTTT
1 AAAAAAAATCGATTTTT
968323 AAAAAAAATCGATTTTT
1 AAAAAAAATCGATTTTT
968340 AA
1 AA
968342 TCCGGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (17 bp):
AAAAAAAATCGATTTTT
Found at i:973675 original size:38 final size:38
Alignment explanation
Indices: 973598--973676 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
973588 GAAATGAATA
* *
973598 TTTACTACATTTTAAGATACTAAAATTATCACAATAGT
1 TTTACTACATATTAAGATACTAAAATTATCACAACAGT
* * *
973636 TTTACTAGATATTAAGATACTACAAA-TATTATAACAGT
1 TTTACTACATATTAAGATACTA-AAATTATCACAACAGT
973674 TTT
1 TTT
973677 TTTGGGGAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 32 0.91
39 3 0.09
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (38 bp):
TTTACTACATATTAAGATACTAAAATTATCACAACAGT
Found at i:977714 original size:13 final size:13
Alignment explanation
Indices: 977698--977726 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
977688 TAATAGCATT
977698 TTTATTTTTAATA
1 TTTATTTTTAATA
977711 TTTATTTTTAATA
1 TTTATTTTTAATA
977724 TTT
1 TTT
977727 TAGTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTTAATA
Found at i:981894 original size:23 final size:23
Alignment explanation
Indices: 981868--981914 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
981858 GTGACCGATT
981868 GAGTGGTAATTCATTTGTCTGTG
1 GAGTGGTAATTCATTTGTCTGTG
981891 GAGTGGTAATTCATTTGTCTGTG
1 GAGTGGTAATTCATTTGTCTGTG
981914 G
1 G
981915 CAGATAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.32, T:0.43
Consensus pattern (23 bp):
GAGTGGTAATTCATTTGTCTGTG
Found at i:992780 original size:20 final size:20
Alignment explanation
Indices: 992757--992808 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
992747 AACGCGATCC
992757 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
992777 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
992797 CCAAAATCGCAA
1 CCAGAATCGCAA
992809 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:992889 original size:20 final size:20
Alignment explanation
Indices: 992864--993057 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
992854 GATTTTCCAT
* *
992864 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
992884 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
992904 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
992924 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
992944 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
992964 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
992984 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
993004 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
993025 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
993045 AATCGCAACGCGA
1 AATCGCAACGCGA
993058 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:992909 original size:40 final size:39
Alignment explanation
Indices: 992860--993057 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
992850 TTGCGATTTT
* ** *
992860 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
992898 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
992939 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
992979 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
993018 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
993058 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:992947 original size:60 final size:60
Alignment explanation
Indices: 992864--993056 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
992854 GATTTTCCAT
* ** * *
992864 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
992924 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
992984 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
993045 AATCGCAACGCG
1 AATCGCAACGCG
993057 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:993477 original size:33 final size:33
Alignment explanation
Indices: 993438--993508 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
993428 TTCACTTAGA
*
993438 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
993471 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
993504 TTTCA
1 TTTCA
993509 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:993648 original size:14 final size:14
Alignment explanation
Indices: 993629--993683 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
993619 AGAATGACTG
993629 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
993643 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
993662 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
993676 TCGCAACG
1 TCGCAACG
993684 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:993666 original size:33 final size:33
Alignment explanation
Indices: 993629--993699 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
993619 AGAATGACTG
**
993629 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
993662 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
993695 TCGCA
1 TCGCA
993700 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:993717 original size:19 final size:19
Alignment explanation
Indices: 993695--993792 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
993685 GAAACCAAAA
*
993695 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
993714 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
993728 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
993747 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
993761 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
993780 TCGCGTTGCGATT
1 TCGCGTTGCGATT
993793 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:993736 original size:14 final size:14
Alignment explanation
Indices: 993717--993806 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
993707 TTTCATTTCG
993717 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
993731 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
993750 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
993764 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
993781 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
993797 CGTTGCGATT
1 CGTTGCGATT
993807 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:993742 original size:33 final size:33
Alignment explanation
Indices: 993700--993814 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
993690 CAAAATCGCA
993700 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
993733 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
993766 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
993799 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
993815 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:995716 original size:92 final size:93
Alignment explanation
Indices: 995511--995889 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
995501 TAGATTGCTT
*
995511 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
995576 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
995604 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
995668 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
995696 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
995760 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
995788 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
995853 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
995881 AGTAAATTT
1 AGTAAATTT
995890 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.65
93 99 0.35
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:995741 original size:185 final size:185
Alignment explanation
Indices: 995511--995891 Score: 728
Period size: 185 Copynumber: 2.1 Consensus size: 185
995501 TAGATTGCTT
995511 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
995576 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
995641 GTATATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
995696 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
995761 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
*
995826 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
995881 AGTAAATTTAT
1 AGTAAATTTAT
995892 CCATTCAAGT
Statistics
Matches: 192, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
184 91 0.47
185 101 0.53
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:995973 original size:19 final size:19
Alignment explanation
Indices: 995933--996061 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
995923 TAGTTTACTT
* *
995933 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
995953 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
995972 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
995991 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
996005 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
996024 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
996038 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
996057 TCGCA
1 TCGCA
996062 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:996012 original size:33 final size:32
Alignment explanation
Indices: 995969--996061 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
995959 CGCGAAACCA
**
995969 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
996001 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
996034 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
996062 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:996059 original size:52 final size:52
Alignment explanation
Indices: 995933--996061 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
995923 TAGTTTACTT
**
995933 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
995985 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
996038 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
996062 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:996079 original size:19 final size:19
Alignment explanation
Indices: 996057--996191 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
996047 GAAACCAAAA
*
996057 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
996076 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
996092 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
996109 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
996125 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
996142 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
996161 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
996181 TCGTGTTGCGA
1 TCGCGTTGCGA
996192 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:996098 original size:14 final size:14
Alignment explanation
Indices: 996079--996135 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
996069 TTTCATTTCG
996079 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
996093 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
996110 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
996126 CGTTGCGATT
1 CGTTGCGATT
996136 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:996104 original size:33 final size:33
Alignment explanation
Indices: 996062--996154 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
996052 CAAAATCGCA
*
996062 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
996095 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
996128 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
996155 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:998113 original size:14 final size:14
Alignment explanation
Indices: 998094--998129 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
998084 ATTGTTTAAT
998094 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
998108 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
998122 TGATTTGT
1 TGATTTGT
998130 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:998252 original size:19 final size:19
Alignment explanation
Indices: 998236--998337 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
998226 AAAAATGACT
998236 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
998255 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
998274 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
998288 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
998307 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
998327 ATCGCAATGCG
1 ATCGCAATGCG
998338 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:998394 original size:19 final size:19
Alignment explanation
Indices: 998370--998639 Score: 346
Period size: 19 Copynumber: 15.2 Consensus size: 19
998360 ATCTCGTTGT
998370 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
998389 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
998408 GA--TTC-TTTCG--TTGC
1 GATTTTCATTTCGCATTGC
998422 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
998441 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
998460 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
998479 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
998498 GATTTTAATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
998517 GA--TTC-TGTCG--TTGC
1 GATTTTCATTTCGCATTGC
998531 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
998550 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
998569 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
998583 GATTTTCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
*
998603 GATTTTCA--T-G--TTGG
1 GATTTTCATTTCGCATTGC
*
998617 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCATTGC
998636 GATT
1 GATT
998640 GTATTTTCCG
Statistics
Matches: 222, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 20 0.09
18 3 0.01
19 134 0.60
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:998406 original size:52 final size:52
Alignment explanation
Indices: 998344--998611 Score: 428
Period size: 52 Copynumber: 5.0 Consensus size: 52
998334 TGCGTTTATA
* *
998344 ATTTCGCATTGCGATTATCTCGTTGTGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
998396 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
998448 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
998505 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
998557 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
998610 AT
1 AT
998612 GTTGGGATTT
Statistics
Matches: 203, Mismatches: 7, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
52 128 0.63
53 17 0.08
54 7 0.03
55 8 0.04
57 43 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:998499 original size:109 final size:104
Alignment explanation
Indices: 998344--998611 Score: 437
Period size: 109 Copynumber: 2.5 Consensus size: 104
998334 TGCGTTTATA
* *
998344 ATTTCGCATTGCGATTATCTCGTTGTGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
998409 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 ATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
998448 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCA
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
998513 TTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
61 TTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
998557 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
998612 GTTGGGATTT
Statistics
Matches: 151, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
104 29 0.19
105 16 0.11
106 6 0.04
107 7 0.05
109 93 0.62
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (104 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:998604 original size:34 final size:33
Alignment explanation
Indices: 998344--998639 Score: 155
Period size: 33 Copynumber: 8.5 Consensus size: 33
998334 TGCGTTTATA
* *
998344 ATTTCGCATTGCGATTATC-TCGTTGTGATTTTC
1 ATTTCGCATTGCGATTCTCAT-GTTGCGATTTTC
*
998377 ATTTCGCATTGCGATTTTCAT-TT-CGCATTGCGATTC
1 ATTTCGCATTGCGATTCTCATGTTGCG-ATT----TTC
*
998413 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
*
998448 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
* * *
998486 ATTTCGCATTGCGATTTTAAT-TT-CGCA-TTGC
1 ATTTCGCATTGCGATTCTCATGTTGCG-ATTTTC
* *
998517 GA-TTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 -ATTTC-G-CATTGCGATTCTCA--T-G--TTGCGATTTTC
998557 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCAT-GTTGCGATTTTC
* *
998590 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTCATGTTGCGATTTTC
*
998624 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
998640 GTATTTTCCG
Statistics
Matches: 220, Mismatches: 12, Indels: 62
0.75 0.04 0.21
Matches are distributed among these distances:
31 9 0.04
32 10 0.05
33 68 0.31
34 30 0.14
35 14 0.06
36 9 0.04
38 60 0.27
39 10 0.05
40 10 0.05
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCATGTTGCGATTTTC
Found at i:1000938 original size:12 final size:12
Alignment explanation
Indices: 1000921--1000945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1000911 TCTTCGGGGA
1000921 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1000933 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1000945 C
1 C
1000946 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1001154 original size:24 final size:24
Alignment explanation
Indices: 1001120--1001166 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1001110 CTGAAACATC
1001120 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1001144 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1001167 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1001877 original size:20 final size:20
Alignment explanation
Indices: 1001849--1002217 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
1001839 AAATTTAAGT
* * * *
1001849 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1001869 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1001889 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1001909 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1001929 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1001949 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1001969 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1001989 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1002009 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1002029 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1002049 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
1002069 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1002089 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1002109 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1002129 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1002149 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1002169 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1002189 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1002209 GTTGCGATT
1 GTTGCGATT
1002218 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1008087 original size:2 final size:2
Alignment explanation
Indices: 1008082--1008106 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1008072 TGTGTGTGTG
1008082 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1008107 TGGTAACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1012244 original size:33 final size:32
Alignment explanation
Indices: 1012168--1012245 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
1012158 TTGAGTTCAT
* *
1012168 ATCGATTATTTTTTAGCTCGAATCAATATCAG
1 ATCGATTATTTTTTAGCTAGAATCAATATCAA
*
1012200 ATTGATTATTTTTTAGCTTAG-ATCAATATCAA
1 ATCGATTATTTTTTAGC-TAGAATCAATATCAA
*
1012232 ATCGGTTGATTTTT
1 ATCGATT-ATTTTT
1012246 GGGTCAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 31 0.79
33 8 0.21
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (32 bp):
ATCGATTATTTTTTAGCTAGAATCAATATCAA
Found at i:1012540 original size:12 final size:12
Alignment explanation
Indices: 1012523--1012547 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1012513 AAGAAAAAAA
1012523 TTTATTATAAAT
1 TTTATTATAAAT
1012535 TTTATTATAAAT
1 TTTATTATAAAT
1012547 T
1 T
1012548 AAAATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATTATAAAT
Found at i:1012878 original size:32 final size:32
Alignment explanation
Indices: 1012832--1012909 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
1012822 CTAACATGAT
1012832 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
1 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
*
1012864 TGAGGGACTGAAATTGAACGAGAGTTAACGAC
1 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
1012896 TGAGGGACTAAAAT
1 TGAGGGACTAAAAT
1012910 CTAATAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.19
Consensus pattern (32 bp):
TGAGGGACTAAAATTGAACGAGAGTTAACGAC
Found at i:1012936 original size:31 final size:31
Alignment explanation
Indices: 1012898--1012965 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1012888 TTAACGACTG
* * *
1012898 AGGGACTAAAATCTAATAGATTGATAACATT
1 AGGGACTAAAATCGAACAGATCGATAACATT
* *
1012929 AGGGACTAATATCGAACAGATCGATAGCATT
1 AGGGACTAAAATCGAACAGATCGATAACATT
1012960 AGGGAC
1 AGGGAC
1012966 CATTTTCCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (31 bp):
AGGGACTAAAATCGAACAGATCGATAACATT
Found at i:1013111 original size:21 final size:22
Alignment explanation
Indices: 1013087--1013127 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1013077 ATTATAAATA
1013087 AAAAATAA-ATTTTTATATTGT
1 AAAAATAACATTTTTATATTGT
*
1013108 AAAAATAACCTTTTTATATT
1 AAAAATAACATTTTTATATT
1013128 AAATTTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAAATAACATTTTTATATTGT
Found at i:1013642 original size:29 final size:28
Alignment explanation
Indices: 1013589--1013649 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
1013579 TTAGACTTAG
*
1013589 ATATTTAATAAATAAAATTAGTTAAATA
1 ATATTTAATAAATAAAATAAGTTAAATA
* *
1013617 ATATTTAAATCAAAT-AAATAATTTAAATT
1 ATATTT-AAT-AAATAAAATAAGTTAAATA
1013646 ATAT
1 ATAT
1013650 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 18 0.64
30 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
ATATTTAATAAATAAAATAAGTTAAATA
Found at i:1018189 original size:60 final size:60
Alignment explanation
Indices: 1018087--1018241 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
1018077 GCATCATGTG
* * * * *
1018087 TCCTCAAAGTATGACCT-TCATTTTAAATTGGTCCTTAAACTTTTAAAT-GTTCCAATTCCA
1 TCCTCAAACTATGA-CTATCATTCTAAATTAGTCCTTAAACTTTTAAATAGCT-CAATTACA
*
1018147 TCC-CTAAACTATGACTATCATTCTAAATTAGT-CTTCAAACTTTTGAATAGCTCAATTACA
1 TCCTC-AAACTATGACTATCATTCTAAATTAGTCCTT-AAACTTTTAAATAGCTCAATTACA
*
1018207 TCCTCAAACTATGAC-ATTCATTCTAAATTGGTCCT
1 TCCTCAAACTATGACTA-TCATTCTAAATTAGTCCT
1018242 CTTTTTGAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
59 7 0.09
60 69 0.85
61 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.38
Consensus pattern (60 bp):
TCCTCAAACTATGACTATCATTCTAAATTAGTCCTTAAACTTTTAAATAGCTCAATTACA
Found at i:1018520 original size:60 final size:59
Alignment explanation
Indices: 1018387--1018523 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 59
1018377 TATTTGCATA
* * ** *
1018387 AATTTTGGGATGAAATTGGAATATAAAAAATTTTGGGTATTAATTTAGAAAAAGGGTAT
1 AATTTAGGGATGAAATTAGAATATAAAAAATTTAAGGTATTAATTTAGAAAAAGAGTAT
* * ** *
1018446 AGTTTAGGGATGAAATTAGAATGTTAAAAAATTTAAGG-ATTAATTTAGAATGATAGTCAT
1 AATTTAGGGATGAAATTAGAAT-ATAAAAAATTTAAGGTATTAATTTAGAAAAAGAGT-AT
*
1018506 AATTTGGGGATGAAATTA
1 AATTTAGGGATGAAATTA
1018524 AATTTTTTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 34 0.53
60 30 0.47
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.35
Consensus pattern (59 bp):
AATTTAGGGATGAAATTAGAATATAAAAAATTTAAGGTATTAATTTAGAAAAAGAGTAT
Found at i:1027103 original size:20 final size:21
Alignment explanation
Indices: 1027050--1027103 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
1027040 AAGTACTACC
* *
1027050 AAATAGAGAGAGAGATTAAGA
1 AAATAGAGAAAGAGATGAAGA
*
1027071 AAATATGA-TAAGAG-TGAAGA
1 AAATA-GAGAAAGAGATGAAGA
1027091 AAATAGAGAAAGA
1 AAATAGAGAAAGA
1027104 AAGGGGGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.07
20 14 0.52
21 9 0.33
22 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (21 bp):
AAATAGAGAAAGAGATGAAGA
Found at i:1032620 original size:17 final size:17
Alignment explanation
Indices: 1032598--1032630 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1032588 ACTCGTTAAA
*
1032598 AACTCGAGTCAAGTTCG
1 AACTCGAATCAAGTTCG
1032615 AACTCGAATCAAGTTC
1 AACTCGAATCAAGTTC
1032631 ATTTAATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (17 bp):
AACTCGAATCAAGTTCG
Found at i:1038654 original size:14 final size:13
Alignment explanation
Indices: 1038619--1038657 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
1038609 TTTAATAATT
1038619 TAAAATTT-AAAC
1 TAAAATTTAAAAC
1038631 TAAAATTTTAAAAC
1 TAAAA-TTTAAAAC
1038645 ATAAAATTTAAAA
1 -TAAAATTTAAAA
1038658 TTATTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 3 0.12
14 11 0.46
15 5 0.21
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAATTTAAAAC
Found at i:1038915 original size:23 final size:24
Alignment explanation
Indices: 1038848--1038916 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
1038838 GTTTAAAATA
* *
1038848 AAAAATAATTATTTATATATTTTAT
1 AAAATTAA-TATTTATATATTTTAG
* *
1038873 AAAATTAATATTAATTTATTTT-G
1 AAAATTAATATTTATATATTTTAG
1038896 AAAATTAA-ATTTATGATATTT
1 AAAATTAATATTTAT-ATATTT
1038917 ATTTATGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 5 0.14
23 13 0.35
24 12 0.32
25 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (24 bp):
AAAATTAATATTTATATATTTTAG
Found at i:1044945 original size:30 final size:30
Alignment explanation
Indices: 1044909--1044974 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
1044899 TTCAAGGGTT
*
1044909 AAATTAATATTTTATCTAAAATCTAAGATC
1 AAATTAATATTTTATATAAAATCTAAGATC
* *
1044939 AAATTAATATTTTATATAAAGTCTGAGATC
1 AAATTAATATTTTATATAAAATCTAAGATC
1044969 AAATTA
1 AAATTA
1044975 GCATTTTGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATTAATATTTTATATAAAATCTAAGATC
Found at i:1050946 original size:40 final size:40
Alignment explanation
Indices: 1050882--1050957 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
1050872 AAACAATCAA
*
1050882 AATGTGGACGTTACCATCCAATATATGAAAGAACCACCAT
1 AATGTGGACGTTACCAACCAATATATGAAAGAACCACCAT
* * * * *
1050922 AATGTGGATGTTACTAACCCATATATGGATGAACCA
1 AATGTGGACGTTACCAACCAATATATGAAAGAACCA
1050958 TCAGAGTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (40 bp):
AATGTGGACGTTACCAACCAATATATGAAAGAACCACCAT
Found at i:1060772 original size:16 final size:17
Alignment explanation
Indices: 1060740--1060776 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1060730 AGGATGTGAT
*
1060740 TATTGTCTTAGTAATTA
1 TATTTTCTTAGTAATTA
1060757 TATTTTCTTA-TAATTA
1 TATTTTCTTAGTAATTA
1060773 -ATTT
1 TATTT
1060777 GAATATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 6 0.32
17 9 0.47
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (17 bp):
TATTTTCTTAGTAATTA
Found at i:1061910 original size:58 final size:59
Alignment explanation
Indices: 1061768--1061936 Score: 232
Period size: 58 Copynumber: 2.8 Consensus size: 59
1061758 TATCAGTTGA
* * * *
1061768 AGTACAGTGGCCGGTGGCAAATGTGATCATTAACTCTAAAAAACAAATTAGAGTACAAATAT
1 AGTATAGTGGCCGGTGACAAATTTGATCATTAACTCT-AAAAA-AAA-TAGAATACAAATAT
*
1061830 AGTATAGTGGCCGGTGACAAATTTGATCATTAACTCT-AAAAAAATAGAATACAGATAT
1 AGTATAGTGGCCGGTGACAAATTTGATCATTAACTCTAAAAAAAATAGAATACAAATAT
* * *
1061888 AGTCTAGTGGCAGGTGACAAATTTGATCATGAACTCTAAAAAAAATAGA
1 AGTATAGTGGCCGGTGACAAATTTGATCATTAACTCTAAAAAAAATAGA
1061937 GTATATATAT
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
58 46 0.47
59 14 0.14
60 4 0.04
62 34 0.35
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (59 bp):
AGTATAGTGGCCGGTGACAAATTTGATCATTAACTCTAAAAAAAATAGAATACAAATAT
Found at i:1066057 original size:24 final size:25
Alignment explanation
Indices: 1066030--1066076 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1066020 TAATTTTTTT
*
1066030 AGTTGAATCAAATT-TTAAAATTCG
1 AGTTAAATCAAATTGTTAAAATTCG
*
1066054 AGTTAAATCAAATTGTTTAAATT
1 AGTTAAATCAAATTGTTAAAATT
1066077 TTTTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (25 bp):
AGTTAAATCAAATTGTTAAAATTCG
Found at i:1066167 original size:2 final size:2
Alignment explanation
Indices: 1066162--1066188 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1066152 TATGTACATG
1066162 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1066189 TACCTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1068864 original size:20 final size:21
Alignment explanation
Indices: 1068818--1068863 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1068808 AGATTATCGA
1068818 TAAAAAATATAAAGAAAATAT
1 TAAAAAATATAAAGAAAATAT
*
1068839 T-TAAAATAT-AAGAAAAT-T
1 TAAAAAATATAAAGAAAATAT
1068857 TAAAAAA
1 TAAAAAA
1068864 AATTAGGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 12 0.55
20 7 0.32
21 1 0.05
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
TAAAAAATATAAAGAAAATAT
Found at i:1070729 original size:16 final size:16
Alignment explanation
Indices: 1070708--1070739 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1070698 ATTATGAGTA
*
1070708 TTTTTTAATATTATAT
1 TTTTTTAATAATATAT
1070724 TTTTTTAATAATATAT
1 TTTTTTAATAATATAT
1070740 GATGATTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTAATAATATAT
Found at i:1077735 original size:27 final size:27
Alignment explanation
Indices: 1077705--1077836 Score: 83
Period size: 27 Copynumber: 4.9 Consensus size: 27
1077695 TAACGGTAAT
*
1077705 AGCAGTAGAACTTATTGCAACACTGGA
1 AGCATTAGAACTTATTGCAACACTGGA
* ***
1077732 AGCATTAAAACTT-TCTGCAACACTATC
1 AGCATTAGAACTTAT-TGCAACACTGGA
* * *
1077759 AGCATTCA-AAC-CAGCTGCAACACT-AA
1 AGCATT-AGAACTTA-TTGCAACACTGGA
* * *
1077785 CAGAAGTAGAACTCATTGCAACACTGGA
1 -AGCATTAGAACTTATTGCAACACTGGA
* *
1077813 AGCATTAGAACTTGTGGCAACACT
1 AGCATTAGAACTTATTGCAACACT
1077837 ACCAGCAATA
Statistics
Matches: 79, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
26 2 0.03
27 73 0.92
28 4 0.05
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (27 bp):
AGCATTAGAACTTATTGCAACACTGGA
Found at i:1082076 original size:29 final size:29
Alignment explanation
Indices: 1082024--1082104 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
1082014 CCGGCCCGGT
* * *
1082024 GATATTTAG-TAATTATTTTGAAAAAGGC
1 GATATTTTGATAATTATTTTTAAAAAGAC
* *
1082052 GATGTTTTGATAATTATTTTTAAAAAGAT
1 GATATTTTGATAATTATTTTTAAAAAGAC
*
1082081 GATATTTTGGTAATTATTTTTAAA
1 GATATTTTGATAATTATTTTTAAA
1082105 CATGTGTGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (29 bp):
GATATTTTGATAATTATTTTTAAAAAGAC
Found at i:1083342 original size:52 final size:49
Alignment explanation
Indices: 1083253--1083356 Score: 181
Period size: 52 Copynumber: 2.1 Consensus size: 49
1083243 CATGATATGT
1083253 TGTATGTTAAAGGAATTATGATGGTATAAGAATTGATAGGAAATATATTA
1 TGTATGTTAAAGGAATTATGATGGTATAAGAATTGATAGGAAATATA-TA
1083303 TGTATGTTAAAGGAATTATGTGATGGTATAAGAATTGATAGGAAATATATA
1 TGTATGTTAAAGGAATTA--TGATGGTATAAGAATTGATAGGAAATATATA
1083354 TGT
1 TGT
1083357 GAAAACAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
50 18 0.35
51 5 0.10
52 29 0.56
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (49 bp):
TGTATGTTAAAGGAATTATGATGGTATAAGAATTGATAGGAAATATATA
Found at i:1083914 original size:23 final size:22
Alignment explanation
Indices: 1083856--1083921 Score: 98
Period size: 21 Copynumber: 3.0 Consensus size: 22
1083846 TATGGACATC
*
1083856 ATTCTACGGGCACTACGG-GCA
1 ATTCTACGGGCACTTCGGTGCA
*
1083877 ATTCTACGGGCACTTTGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1083899 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
1083922 TTTATACGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 16 0.40
22 10 0.25
23 14 0.35
ACGTcount: A:0.20, C:0.26, G:0.29, T:0.26
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:1087046 original size:20 final size:19
Alignment explanation
Indices: 1087021--1087060 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1087011 TTTCTGGGCA
* *
1087021 AGGGGAATCGGTACCCATTC
1 AGGGGAACCGATACCC-TTC
1087041 AGGGGAACCGATACCCTTC
1 AGGGGAACCGATACCCTTC
1087060 A
1 A
1087061 AACGAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (19 bp):
AGGGGAACCGATACCCTTC
Found at i:1088743 original size:22 final size:22
Alignment explanation
Indices: 1088715--1088780 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
1088705 TATGGACATC
*
1088715 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
*
1088737 ATTCTACGGGCACTTTGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1088759 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1088781 TTTATATGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:1089927 original size:29 final size:29
Alignment explanation
Indices: 1089883--1089986 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 29
1089873 GACCCGGCCC
* *
1089883 GGTGATATTTTAGTAATTATTTTGAAAAA
1 GGTGATATTTTGGTAATTATTTTAAAAAA
* *
1089912 GGTGATGTTTTGGTAATTATTTTTAAAAA
1 GGTGATATTTTGGTAATTATTTTAAAAAA
*
1089941 GGTTATATTTTGGTAATTATTTTAAAAAA
1 GGTGATATTTTGGTAATTATTTTAAAAAA
* * *
1089970 TGTGTTATTTTCGTAAT
1 GGTGATATTTTGGTAAT
1089987 AGTTGACTGT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.49
Consensus pattern (29 bp):
GGTGATATTTTGGTAATTATTTTAAAAAA
Found at i:1097657 original size:38 final size:38
Alignment explanation
Indices: 1097606--1097679 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
1097596 TTATAACCAT
* *
1097606 GCATATAAATTTACATACTGCAAAGGAGAACATGTCAA
1 GCATATAAATTTACATACCGCAAAAGAGAACATGTCAA
1097644 GCATATAAATTTACATACCGCAAAAGAGAACATGTC
1 GCATATAAATTTACATACCGCAAAAGAGAACATGTC
1097680 GTCCATTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.23
Consensus pattern (38 bp):
GCATATAAATTTACATACCGCAAAAGAGAACATGTCAA
Found at i:1098617 original size:18 final size:18
Alignment explanation
Indices: 1098594--1098643 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1098584 GAAAGATTCA
1098594 TCATCTGTAGGTAATCGT
1 TCATCTGTAGGTAATCGT
1098612 TCATCTGTAGGTAATCGT
1 TCATCTGTAGGTAATCGT
1098630 TCATCTGTAGGTAA
1 TCATCTGTAGGTAA
1098644 ATCCTTCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
TCATCTGTAGGTAATCGT
Done.